@MetalGamerFil
Please supply the information requested in
https://retropie.org.uk/forum/topic/3/read-this-first
In which mode are you using the controller?
I had some trouble configuring mine with a couple of buttons when it was in X-input mode (X + Start when turning on the controller). Some of buttons were showing up as analog axes instead of button presses. I solved it by changing the mode to either Switch mode (Y + Start) or D-input (B + Start) and re-configuring the controller.
I think part of the problem is EmulationStation doesn't want you to use an Axis when configuring certain buttons. Not sure if this could be fixed in the auto configuration. I believe you could manually edit the controller config to get around that though.